fix input file regexes

lib/WorkflowMain.groovy

@@ -49,12 +49,6 @@ class WorkflowMain {
             Nextflow.error("Please provide an input sdrf to the pipeline e.g. '--input *.sdrf.csv'")
         }
 
-        // Check input has been provided
-        if (!params.outdir) {
-            log.error "Please provide an outdir to the pipeline e.g. '--outdir ./results'"
-            System.exit(1)
-        }
-
         // check fasta database has been provided
         if (!params.database) {
             Nextflow.error("Please provide an fasta database to the pipeline e.g. '--database *.fasta'")

modules/local/openms/epifany/main.nf

@@ -2,8 +2,6 @@ process EPIFANY {
     label 'process_medium'
     label 'openms'
 
-    publishDir "${params.outdir}"
-
     conda "bioconda::openms=2.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :

nextflow_schema.json

@@ -17,7 +17,7 @@
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/tsv",
-                    "pattern": "^\\S+\\.tsv$",
+                    "pattern": "^\\S+\\.(?:tsv|sdrf)$",
                     "description": "URI/path to an [SDRF](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) file (.sdrf.tsv) **OR** [OpenMS-style experimental design](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html#details) with paths to spectra files (.tsv)",
                     "help_text": "Input is specified by using a path or URI to a PRIDE Sample to Data Relation Format file (SDRF), e.g. as part of a submitted and\nannotated PRIDE experiment (see [here](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) for examples). Input files will be downloaded and cached from the URIs specified in the SDRF file.\nAn OpenMS-style experimental design will be generated based on the factor columns of the SDRF. The settings for the\nfollowing parameters will currently be overwritten by the ones specified in the SDRF:\n\n    * `fixed_mods`,\n    * `variable_mods`,\n    * `precursor_mass_tolerance`,\n    * `precursor_mass_tolerance_unit`,\n    * `fragment_mass_tolerance`,\n    * `fragment_mass_tolerance_unit`,\n    * `fragment_method`,\n    * `enzyme`\n  You can also specify an [OpenMS-style experimental design](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html#details) directly (.tsv ending). In this case, the aforementioned parameters have to be specified or defaults will be used.",
                     "fa_icon": "fas fa-file-csv"
@@ -70,6 +70,10 @@
             "properties": {
                 "database": {
                     "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/fasta",
+                    "pattern": "^\\S+\\.(?:fasta|fa)$",
                     "description": "The `fasta` protein database used during database search. *Note:* For DIA data, it must not contain decoys.",
                     "fa_icon": "fas fa-file",
                     "help_text": "Since the database is not included in an SDRF, this parameter always needs to be given to specify the input protein database\nwhen you run the pipeline. Remember to include contaminants (and decoys if not in DIA mode and if not added in the pipeline with [`--add_decoys`](#add_decoys))\n\n```bash\n--database '[path to fasta protein database]'\n```"